Additionally, we support and expand upon the hypothesis that
X inactivation is primarily driven by gene loss on the Y. Using linear discriminant analysis, we show that
X-inactivation status can successfully classify 90 % of
X-linked genes into those with functional or nonfunctional Y
homologs.
For example, clusters containing genes that are upregulated during the course of ES cell differentiation (Table 3) include in order of time of expression: cluster 30 that represents genes which take part in the formation of the three embryonic germ layers during gastrulation, i.e., Goosecoid, Cerberus like 1
homolog, Wnt3, Mesp1, Mixl1, mEomes and Even - skipped 1; cluster 15 containing molecular regulators of early mesoderm development including Bmp2, Bmp5, Msx1, Msx2, Cripto, Tbx20, Hey2, Smad6, Vegfr2 (Kdr), Foxf1 and Hand1; cluster 20, which comprises regulatory and structural genes linked to hemopoiesis such as Gata1, Nfe2, Klf1, Tie1, hemoglobins (Hba -
x, Hbb - b1) and Glycophorin A; cluster 12, which is rich in genes involved in cardiac development, e.g., Mef2c, Myl4, cardiac Troponin T2, Tropomodulin 1, myosin binding protein C, Bves, Angiopoietin 1 and Angiopoietin 2; and, cluster 4, which consists mostly of genes associated with neuronal development and differentiation, for example, Neurog1, Neurog2, Olig2, Nkx6.1, Neurod4, Pou3f2, Pou3f4, Cacna2d3, Cacng4, Kcnq2 and EphA5.